Research workbench
Crystal structure of human insulin-degrading enzyme in complex with amylin
Analyse Crystal structure of human insulin-degrading enzyme in complex with amylin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G48
- Type
- protein
- Length
- 1,969 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-degrading enzyme; Islet amyloid polypeptide
- EC
- 3.4.24.56
- UniProt
- Q5T5N2, P10997
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 968 | 44% helix, 20% strand | Q5T5N2 |
| B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 966 | 43% helix, 21% strand | Q5T5N2 |
| C | Islet amyloid polypeptide | protein | 18 | 17% helix, 17% strand | P10997 |
| D | Islet amyloid polypeptide | protein | 17 | 0% helix, 18% strand | P10997 |
Ligands and binding sites
- DIO · 1,4-diethylene dioxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.85 | 0.86 | 98 | empty |
| 2 | 1109 | 0.81 | 0.82 | 114 | DIO |
| 3 | 688 | 0.80 | 0.84 | 73 | DIO |
| 4 | 795 | 0.76 | 0.80 | 77 | empty |
| 5 | 442 | 0.76 | 0.85 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1520 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1166 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1030 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 2G48 · crystal structure of human insulin-degrading enzyme in complex with amylin · the same entry in another collection · chain A against A, TM-score 1.00
- P10997 · AlphaFold monomer V2.0 prediction for islet amyloid polypeptide (P10997) · a predicted model of the same protein · chain C against A, TM-score 0.23
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q5T5N2
- Every structure of UniProt P10997
- Elsewhere: RCSB PDB 2G48 · PDBe 2G48 · UniProt Q5T5N2 · UniProt P10997
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